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The value of coral reefs, both for the biosphere and human species is well established. However, corals throughout the world are suffering from an onslaught of both natural and human disturbances that in concert over the last few decades have degraded or destroyed many reefs. Hence, there arises a need for an effective method to monitor and assess the state of coral reefs.This book explores the potential use of fluorescence pigments including chlorophyll as coral health indices by monitoring the fluorescence signals of healthy and diseased specimens of corals and the development of a Laser Induced Multispectral fluorescence Imaging System (LIMFIS). LIMFIS can acquire information over large coral cover and detect coral bleaching at the initial stage. This work also identified the different clades of symbiotic Zooxanthellae on corals and provide information on the nucleotide sequences deposited in GenBank database.